[mira_talk] mira bambus mira
- From: Davide Sassera <davide.sassera@xxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Mon, 21 Mar 2011 16:04:10 +0100
Dear Bastien,
Thanks for answering all our questions, it's just great.
My problem, briefly, is: can I do mira --> bambus --> mira? is it
useful? how should I do it?
More in detail here is the situation I'm facing:
I'm currently assemblying a 3.5 Mb genome from 1 solexa lane (28M reads)
and 3/4 454 paired gs-flx plate (3kb library).
I did a denovo assembly with the 454 and 5 M solexa reads (memory
constraints).
Then I did two mappings with the remaining solexa reads (second mapping
based on contigs generated by the first mapping).
I checked the last mapping with gap4 and joined down to 100 contigs.
I then used these 100 to create a scaffold with bambus.
I got three main scaffolds, as follows.
scaff_100 67 2983086 1069841
scaff_101 9 351491 353698
scaff_99 3 156135 157239
The bambus results allowed me to go down to 84 contigs on gap4.
I cannot join more than this, I assume because I have gaps between the
contigs.
I now feel I could elongate the 84 contigs I have with a novel mapping,
but I'm not sure on how to proceed:
Should I use the 84 contigs as they are and hope that a novel mapping
adds the reads that will allow me to join them?
Or should I use the scaffold generated by bambus using print_scaff? This
second option has the advantage of piloting the joins towards what
bambus says, but bambus puts a stretch on Ns between two contigs. How
does mira handle this? can mira use the Ns to join the contigs or not?
thanks in advance
Davide
--
Davide Sassera
Sezione di Patologia Generale e Parassitologia
Dipartimento di Patologia Animale,
Igiene e Sanità Pubblica Veterinaria
Facoltà di Veterinaria
Università degli Studi di Milano
Via Celoria 10, 20133, Milano, ITALY
Tel: +39 0250318094
Fax: +39 0250318095
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